Creating the manifest file myself, with the bare essentials fixes the issue:

Manifest-Version: 1.0
Main-Class: com.example.MyMainClass

With more investigation I'm sure I could have got the dynamic meta-file creation working with Ant as I know other people do - there must be some peculiarity in the combination of my ant version (1.6.2), java version (1.4.2_07) and perhaps the current phase of the moon.

Notes:
Parsing of the Meta-inf file has been an issue that has come-up, been fixed and then come-up again for sun. See: Bug Id: 4991229. If you can work out if this bug exists in the your (or my) version of the Java SE you have more patience that me.